Think Perl 6 teaches introductory programming and computer science, using Perl 6 as the language.

Learning Perl 6 isn't done yet, so it's hard to tell, but it seems to be along the same lines of Think Perl 6, targeting absolute programming beginners who don't know variables, loops, scopes etc. are. Maybe more focused on learning programming, and less on computer science.

Perl 6 Fundamentals assumes that you already know how to program, and you know the basic constructs (variables, functions, classes, objects, recursion), but have no experience in Perl 6. It aims to show practical examples, in the hopes of inspiring your and teaching you to write practical Perl 6 code.

I can't comment on Andrew Shitov's books, because I haven't read them yet. Perl 6 at a Glance by Andrew Shitov teaches the Perl 6 basics point by point, using one to three-line examples for each feature. In contrast, Perl 6 Fundamentals shows and develops larger, somewhat practical examples, and explains the features used along the way.

P.S. I'll post on perlmonks once "Perl 6 Fundamentals" is available for sale.